Examples with SageCommandBuilder com.hartwig.pipeline.calling.sage.SageCommandBuilder used on opensource projects

Example 1 with SageCommandBuilder

use of com.hartwig.pipeline.calling.sage.SageCommandBuilder in project pipeline5 by hartwigmedical.

the class SageRerunOld method execute.

@Override
public VirtualMachineJobDefinition execute(final InputBundle inputs, final RuntimeBucket runtimeBucket, final BashStartupScript commands, final RuntimeFiles executionFlags) {
    // Inputs
    final String set = inputs.get("set").inputValue();
    final String tumorSampleName = inputs.get("tumor_sample").inputValue();
    final String referenceSampleName = inputs.get("ref_sample").inputValue();
    final InputFileDescriptor remoteTumorFile = inputs.get("tumor_cram");
    final InputFileDescriptor remoteReferenceFile = inputs.get("ref_cram");
    final InputFileDescriptor remoteTumorIndex = remoteTumorFile.index();
    final InputFileDescriptor remoteReferenceIndex = remoteReferenceFile.index();
    final String localTumorFile = localFilename(remoteTumorFile);
    final String localReferenceFile = localFilename(remoteReferenceFile);
    final String localTumorBam = CONVERT_TO_BAM ? localTumorFile.replace("cram", "bam") : localTumorFile;
    final String localReferenceBam = CONVERT_TO_BAM ? localReferenceFile.replace("cram", "bam") : localReferenceFile;
    final ResourceFiles resourceFiles = ResourceFilesFactory.buildResourceFiles(RefGenomeVersion.V37);
    // Download tumor
    commands.addCommand(() -> remoteTumorFile.toCommandForm(localTumorFile));
    commands.addCommand(() -> remoteTumorIndex.toCommandForm(localFilename(remoteTumorIndex)));
    // Download normal
    commands.addCommand(() -> remoteReferenceFile.toCommandForm(localReferenceFile));
    commands.addCommand(() -> remoteReferenceIndex.toCommandForm(localFilename(remoteReferenceIndex)));
    final SageCommandBuilder sageCommandBuilder = new SageCommandBuilder(resourceFiles).addReference(referenceSampleName, localReferenceBam).addTumor(tumorSampleName, localTumorBam);
    if (PANEL_ONLY) {
        sageCommandBuilder.panelOnly();
    }
    if (inputs.contains("rna")) {
        final InputFileDescriptor remoteRnaBam = inputs.get("rna");
        final InputFileDescriptor remoteRnaBamIndex = remoteRnaBam.index();
        final String localRnaBam = localFilename(remoteRnaBam);
        // Download rna
        commands.addCommand(() -> remoteRnaBam.toCommandForm(localRnaBam));
        commands.addCommand(() -> remoteRnaBamIndex.toCommandForm(localFilename(remoteRnaBamIndex)));
        // Add to sage application
        sageCommandBuilder.addReference(referenceSampleName + "NA", localRnaBam);
    }
    // Convert to bam if necessary
    if (!localTumorFile.equals(localTumorBam)) {
        commands.addCommands(cramToBam(localTumorFile));
    }
    if (!localReferenceFile.equals(localReferenceBam)) {
        commands.addCommands(cramToBam(localReferenceFile));
    }
    SageApplication sageApplication = new SageApplication(sageCommandBuilder);
    SageSomaticPostProcess sagePostProcess = new SageSomaticPostProcess(tumorSampleName, resourceFiles);
    SubStageInputOutput sageOutput = sageApplication.andThen(sagePostProcess).apply(SubStageInputOutput.empty(tumorSampleName));
    commands.addCommands(sageOutput.bash());
    // 8. Archive targeted output
    final GoogleStorageLocation archiveStorageLocation = sageArchiveDirectory(set);
    final OutputFile filteredOutputFile = sageOutput.outputFile();
    final OutputFile filteredOutputFileIndex = filteredOutputFile.index(".tbi");
    final OutputFile unfilteredOutputFile = sageApplication.apply(SubStageInputOutput.empty(tumorSampleName)).outputFile();
    final OutputFile unfilteredOutputFileIndex = unfilteredOutputFile.index(".tbi");
    commands.addCommand(() -> filteredOutputFile.copyToRemoteLocation(archiveStorageLocation));
    commands.addCommand(() -> filteredOutputFileIndex.copyToRemoteLocation(archiveStorageLocation));
    commands.addCommand(() -> unfilteredOutputFile.copyToRemoteLocation(archiveStorageLocation));
    commands.addCommand(() -> unfilteredOutputFileIndex.copyToRemoteLocation(archiveStorageLocation));
    commands.addCommand(() -> bqrFile(tumorSampleName, "png").copyToRemoteLocation(archiveStorageLocation));
    commands.addCommand(() -> bqrFile(tumorSampleName, "tsv").copyToRemoteLocation(archiveStorageLocation));
    commands.addCommand(() -> bqrFile(referenceSampleName, "png").copyToRemoteLocation(archiveStorageLocation));
    commands.addCommand(() -> bqrFile(referenceSampleName, "tsv").copyToRemoteLocation(archiveStorageLocation));
    // Store output
    commands.addCommand(new OutputUpload(GoogleStorageLocation.of(runtimeBucket.name(), "sage"), executionFlags));
    return VirtualMachineJobDefinition.sageSomaticCalling(commands, ResultsDirectory.defaultDirectory());
}

Example 2 with SageCommandBuilder

use of com.hartwig.pipeline.calling.sage.SageCommandBuilder in project pipeline5 by hartwigmedical.

the class SageCreatePonData method execute.

@Override
public VirtualMachineJobDefinition execute(final InputBundle inputs, final RuntimeBucket runtimeBucket, final BashStartupScript startupScript, final RuntimeFiles executionFlags) {
    final ResourceFiles resourceFiles = ResourceFilesFactory.buildResourceFiles(RefGenomeVersion.V37);
    final InputFileDescriptor remoteReferenceFile = inputs.get("reference");
    final InputFileDescriptor remoteReferenceIndex = remoteReferenceFile.index();
    final String localReferenceFile = localFilename(remoteReferenceFile);
    final String localReferenceBam = localReferenceFile.replace("cram", "bam");
    final String referenceSampleName = inputs.get("referenceSample").inputValue();
    // Download latest jar file
    // startupScript.addCommand(() -> format("gsutil -u hmf-crunch cp %s %s",
    // "gs://batch-sage-validation/resources/sage.jar",
    // "/opt/tools/sage/" + Versions.SAGE + "/sage.jar"));
    // Download normal
    startupScript.addCommand(() -> remoteReferenceFile.toCommandForm(localReferenceFile));
    startupScript.addCommand(() -> remoteReferenceIndex.toCommandForm(localFilename(remoteReferenceIndex)));
    final SageCommandBuilder sageCommandBuilder = new SageCommandBuilder(resourceFiles).ponMode(referenceSampleName, localReferenceBam);
    final SageApplication sageApplication = new SageApplication(sageCommandBuilder);
    // Convert to bam if necessary
    if (!localReferenceFile.equals(localReferenceBam)) {
        startupScript.addCommands(cramToBam(localReferenceFile));
    }
    // Run post processing (NONE for germline)
    final SubStageInputOutput postProcessing = sageApplication.apply(SubStageInputOutput.empty(referenceSampleName));
    startupScript.addCommands(postProcessing.bash());
    // Store output
    startupScript.addCommand(new OutputUpload(GoogleStorageLocation.of(runtimeBucket.name(), "sage"), executionFlags));
    return VirtualMachineJobDefinition.sageSomaticCalling(startupScript, ResultsDirectory.defaultDirectory());
}